Research workbench
Crystal structure of the wild type halophilic malate dehydrogenase in the apo form
Analyse Crystal structure of the wild type halophilic malate dehydrogenase in the apo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D3A
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Halophilic malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q07841
- Ligands
- NA, CL
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Halophilic malate dehydrogenase (EC 1.1.1.37) | protein | 303 | 48% helix, 20% strand | Q07841 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.65 | 0.76 | 49 | empty |
| 2 | 472 | 0.65 | 0.77 | 45 | empty |
| 3 | 101 | 0.38 | 0.76 | 10 | empty |
| 4 | 67 | 0.36 | 0.77 | 16 | empty |
| 5 | 88 | 0.35 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2292 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 1D3A · Crystal structure of the wild type halophilic malate dehydrogenase in the apo form · the same entry in another collection · chain A against A, TM-score 1.00
- Q07841 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (Q07841) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q07841
- Elsewhere: RCSB PDB 1D3A · PDBe 1D3A · UniProt Q07841
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